Professor Philip Hugenholtz
Professor
School of Chemistry and Molecular Biosciences, Faculty of Science
| Featured projects | Duration |
|---|---|
|
High-throughput sequencing of protein variant libraries Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2023 |
Publications
Book Chapters
Davín, Adrián A., Schrempf, Dominik, Williams, Tom A., Hugenholtz, Philip and Szöllősi, Gergely J. (2022). Relative time inference using lateral gene transfers. Environmental microbial evolution: methods and protocols. (pp. 75-94) edited by Haiwei Luo. New York, United States: Humana Press. doi: 10.1007/978-1-0716-2691-7_4
Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2018). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Gene probes: principles and protocols. (pp. 029-042) edited by Marilena Aquino de Muro and Ralph Rapley. New Jersey, United States: Humana Press. doi: 10.1385/1-59259-238-4:029
Sly, Lindsay I. and Hugenholtz, Philip (2015). Blastomonas: ProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceae. Bergey's manual of systematics of archaea and bacteria. (pp. 1-7) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm00918
Sly, Lindsay I. and Hugenholtz, Philip (2015). Blastobacter: ProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceae. Bergey's manual of systematics of archaea and bacteria. (pp. 1-11) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm00800
Patel, Bharat K. C. and Hugenholtz, Philip (2015). Anaerobaculum. Bergey's Manual of Systematics of Archaea and Bacteria. (pp. 1-7) Chichester, United Kingdom: John Wiley & Sons. doi: 10.1002/9781118960608.gbm01254
Tringe, Susannah G. and Hugenholtz, Philip (2011). The enduring legacy of small subunit rRNA in microbiology. Handbook of molecular microbial ecology I: metagenomics and complementary approaches. (pp. 123-128) Hoboken, New Jersey, USA: John Wiley & Sons. doi: 10.1002/9781118010518.ch15
Podar, Mircea, Keller, Martin and Hugenholtz, Philip (2009). Single cell whole genome amplifications of uncultivated organisms. Uncultivated microorganisms. (pp. 83-100) edited by Slava S. Epstein. Heidelberg, Germany: Springer. doi: 10.1007/7171_2008_10
Podar, Mircea, Keller, Martin and Hugenholtz, Philip (2009). Single cell whole genome amplification of uncultivated organisms. Uncultivated microorganisms. (pp. 241-256) edited by Slava S. Epstein. Heidelberg, Germany: Springer . doi: 10.1007/978-3-540-85465-4_10
Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus IV. Blastobacter Zavarzin 1961, 962AL emend. Sly 1985, 44. Bergey's manual of systematic bacteriology. (pp. 452-459) edited by D. J. Brenner, N. R. Krieg and J. T. Staley. New York, U.S.A.: Springer.
Sly, Lindsay I. and Hugenholtz, Philip (2005). Genus II. Blastomonas. Sly and Cahill 1997, 567VP emend. Hiraishi, Kuraishi and Kawahara 2000a. 1117. Bergey's manual of systematic bacteriology: The proteobacteria. Part C. The alpha-, beta-, delta-, and epsilonproteobacteria. (pp. 258-263) edited by D. J. Brenner, N. R. Krieg and J. T. Staley. New York, U.S.A.: Springer. doi: 10.1007/0-387-29298-5_70
Tyson, Gene W. and Hugenholtz, Philip (2005). Environmental shotgun sequencing. Encyclopedia of genetics, genomics, proteomics, and bioinformatics. (pp. 1386-1391) edited by Lynn B. Jorde. West Sussex, U.K.: John Wiley & Sons. doi: 10.1002/047001153X.g205313
Baldauf, S.L., Bhattacharya, D., Cockrill, J., Hugenholtz, Philip, Pawlowski, J. and Simpson, A.G. (2004). The tree of life: An overview. Assembling the tree of life. (pp. 43-75) New York: Oxford University Press.
Hugenholtz, P., Tyson, G. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH). Gene Probes - Principles and Protocols. (pp. 1-17) edited by Aquino de Muro. M and Rapley. R. London: Humana Press.
Journal Articles
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2025). Microbial solutions must be deployed against climate catastrophe. Nature Reviews Microbiology, 2 (1) 23, 1-2. doi: 10.1038/s41579-024-01123-0
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Nature Microbiology, 9 (12), 3084-3085. doi: 10.1038/s41564-024-01861-0
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Biodiversity, 3 (1) 34. doi: 10.1038/s44185-024-00066-2
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Sustainable Agriculture, 2 (1) 23. doi: 10.1038/s44264-024-00033-1
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Haggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadege Adouke, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Fems Microbiology Ecology, 100 (11) ARTN fiae144. doi: 10.1093/femsec/fiae144
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Haggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadege Adouke, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Isme Journal, 18 (1) ARTN wrae219. doi: 10.1093/ismejo/wrae219
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Climate Action, 3 (1) 102. doi: 10.1038/s44168-024-00179-1
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. npj Biofilms and Microbiomes, 10 (1) 122. doi: 10.1038/s41522-024-00591-9
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Communications Earth and Environment, 5 (1) 672. doi: 10.1038/s43247-024-01817-6
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Communications Biology, 7 (1) 1466. doi: 10.1038/s42003-024-07108-2
Peixoto, Raquel, Voolstra, Christian R., Stein, Lisa Y., Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A., Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P., Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T., Ventosa, Antonio, Bavoil, Patrik M., Miller, Virginia and Gilbert, Jack A. (2024). Microbial solutions must be deployed against climate catastrophe. Nature Communications, 15 (1) 9637. doi: 10.1038/s41467-024-53680-w
Venter, Stephanus N., Rodriguez-R, Luis M., Chuvochina, Maria, Palmer, Marike, Hugenholtz, Philip and Steenkamp, Emma T. (2024). Options and considerations for validation of prokaryotic names under the SeqCode. Systematic and Applied Microbiology, 47 (6) 126554. doi: 10.1016/j.syapm.2024.126554
Williams, Tom A., Davin, Adrian A., Szánthó, Lénárd L., Stamatakis, Alexandros, Wahl, Noah A., Woodcroft, Ben J., Soo, Rochelle M., Eme, Laura, Sheridan, Paul O., Gubry-Rangin, Cecile, Spang, Anja, Hugenholtz, Philip and Szöllősi, Gergely J. (2024). Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. The ISME Journal, 18 (1) wrae129. doi: 10.1093/ismejo/wrae129
Mussig, Aaron J., Chaumeil, Pierre-Alain, Chuvochina, Maria, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2024). Putative genome contamination has minimal impact on the GTDB taxonomy. Microbial Genomics, 10 (5) 001256. doi: 10.1099/mgen.0.001256
Yu Jiao, Jian-, Abdugheni, Rashidin, Zhang, Dao-Feng, Ahmed, Iftikhar, Ali, Mukhtiar, Chuvochina, Maria, Dedysh, Svetlana N, Dong, Xiuzhu, Göker, Markus, Hedlund, Brian P, Hugenholtz, Philip, Jangid, Kamlesh, Liu, Shuang-Jiang, Moore, Edward R B, Rao, Manik Prabhu Narsing, Oren, Aharon, Rossello-Mora, Ramon, Rekadwad, Bhagwan Narayan, Salam, Nimaichand, Shu, Wensheng, Sutcliffe, Iain C, Teo, Wee Fei Aaron, Trujillo, Martha E, Venter, Stephanus N, Whitman, William B, Zhao, Guoping and Li, Wen-Jun (2024). Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematics (BISMiS) in addressing challenges in the meta-data era. National Science Review, 11 (7) nwae168, nwae168. doi: 10.1093/nsr/nwae168
Bromfield, Jacoba I., Zaugg, Julian, Straw, Rodney C., Cathie, Julia, Krueger, Annika, Sinha, Debottam, Chandra, Janin, Hugenholtz, Philip and Frazer, Ian H. (2024). Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs. mSphere, 9 (4) e0055523. doi: 10.1128/msphere.00555-23
Miliotis, Georgios, Sengupta, Pratyay, Hameed, Asif, Chuvochina, Maria, McDonagh, Francesca, Simpson, Anna C., Parker, Ceth W., Singh, Nitin K., Rekha, Punchappady D., Morris, Dearbháile, Raman, Karthik, Kyrpides, Nikos C., Hugenholtz, Philip and Venkateswaran, Kasthuri (2024). Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov. mBio, 15 (4) e0018124. doi: 10.1128/mbio.00181-24
Budden, Kurtis F, Shukla, Shakti D, Bowerman, Kate L, Vaughan, Annalicia, Gellatly, Shaan L, Wood, David L A, Lachner, Nancy, Idrees, Sobia, Rehman, Saima Firdous, Faiz, Alen, Patel, Vyoma K, Donovan, Chantal, Alemao, Charlotte A, Shen, Sj, Amorim, Nadia, Majumder, Rajib, Vanka, Kanth S, Mason, Jazz, Haw, Tatt Jhong, Tillet, Bree, Fricker, Michael, Keely, Simon, Hansbro, Nicole, Belz, Gabrielle T, Horvat, Jay, Ashhurst, Thomas, van Vreden, Caryn, McGuire, Helen, Fazekas de St Groth, Barbara ... Hansbro, Philip M (2024). Faecal microbial transfer and complex carbohydrates mediate protection against COPD. Gut, 73 (5), gutjnl-2023. doi: 10.1136/gutjnl-2023-330521
Jones, Adrienne L., Pratt, Carrie J., Meili, Casey H., Soo, Rochelle M., Hugenholtz, Philip, Elshahed, Mostafa S. and Youssef, Noha H. (2024). Anaerobic gut fungal communities in marsupial hosts. Mbio, 15 (2) e0337023. doi: 10.1128/mbio.03370-23
Field, Christian J., Bowerman, Kate L. and Hugenholtz, Philip (2024). Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microbial Genomics, 10 (1) 001176. doi: 10.1099/mgen.0.001176
Peixoto, Raquel, Voolstra, Christian R, Stein, Lisa Y, Hugenholtz, Philip, Salles, Joana Falcao, Amin, Shady A, Häggblom, Max, Gregory, Ann, Makhalanyane, Thulani P, Wang, Fengping, Agbodjato, Nadège Adoukè, Wang, Yinzhao, Jiao, Nianzhi, Lennon, Jay T, Ventosa, Antonio, Bavoil, Patrik M, Miller, Virginia and Gilbert, Jack A (2024). Microbial solutions must be deployed against climate catastrophe. Sustainable Microbiology, 1 (1). doi: 10.1093/sumbio/qvae029
Leong, Lex E X, Denman, Stuart E, Kang, Seungha, Mondot, Stanislas, Hugenholtz, Philip and McSweeney, Chris S (2023). - Invited Review - Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum Synergistota. Animal bioscience, 37 (2), 396-403. doi: 10.5713/ab.23.0351
de la Haba, Rafael R., Arahal, David R., Sánchez-Porro, Cristina, Chuvochina, Maria, Wittouck, Stijn, Hugenholtz, Philip and Ventosa, Antonio (2023). A long-awaited taxogenomic investigation of the family Halomonadaceae. Frontiers in Microbiology, 14 1293707, 1-28. doi: 10.3389/fmicb.2023.1293707
Zhou, Joyce, Boyd, Joel A., Nyeverecz, Bozica, Vivian, Charlotte, Angel, Nicola, Wood, David L. A., Hugenholtz, Philip, Tyson, Gene W., Krause, Lutz and Ó Cuív, Páraic (2023). Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humans. BMC Research Notes, 16 (1) 174, 1-4. doi: 10.1186/s13104-023-06447-3
Song, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Zaugg, Julian, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). Corrigendum: 'A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia'. Microbial Genomics, 9 (8) 001092. doi: 10.1099/mgen.0.001092
McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash and Knight, Rob (2023). Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology, 42 (5), 715-718. doi: 10.1038/s41587-023-01845-1
Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Skarshewski, Adam, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2023). Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes. FEMS Microbiology Letters, 370 fnad071, 1-33. doi: 10.1093/femsle/fnad071
Williams, Tom A., Davín, Adrián A., Morel, Benoit, Szánthó, Lénárd L., Spang, Anja, Stamatakis, Alexandros, Hugenholtz, Philip and Szöllősi, Gergely J. (2023). Parameter estimation and species tree rooting using ALE and GeneRax. Genome Biology and Evolution, 15 (7) evad134. doi: 10.1093/gbe/evad134
Krco, Stefan, Davis, Samuel J., Joshi, Pallav, Wilson, Liam A., Monteiro Pedroso, Marcelo, Douw, Andrew, Schofield, Christopher J., Hugenholtz, Philip, Schenk, Gerhard and Morris, Marc T. (2023). Structure, function, and evolution of metallo-β-lactamases from the B3 subgroup—emerging targets to combat antibiotic resistance. Frontiers in Chemistry, 11 1196073, 1196073. doi: 10.3389/fchem.2023.1196073
Song, Young C., Holland, Sophie I., Lee, Matthew, Chen, Gao, Löffler, Frank E., Manefield, Michael J., Hugenholtz, Philip and Kappler, Ulrike (2023). A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia. Microbial Genomics, 9 (6) 001039, 1-15. doi: 10.1099/mgen.0.001039
Volmer, James G., Soo, Rochelle M., Evans, Paul N., Hoedt, Emily C., Astorga Alsina, Ana L., Woodcroft, Benjamin J., Tyson, Gene W., Hugenholtz, Philip and Morrison, Mark (2023). Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, 21 (1) 59, 1-17. doi: 10.1186/s12915-023-01524-2
Blyton, Michaela D. J., Pascoe, Jack, Hynes, Emily, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2023). The koala gut microbiome is largely unaffected by host translocation but rather influences host diet. Frontiers in Microbiology, 14 1085090, 1-13. doi: 10.3389/fmicb.2023.1085090
Bromfield, Jacoba Isobella, Hugenholtz, Philip, Frazer, Ian Hector, Khosrotehrani, Kiarash and Chandra, Janin (2023). Targeting Staphylococcus aureus dominated skin dysbiosis in actinic keratosis to prevent the onset of cutaneous squamous cell carcinoma: Outlook for future therapies?. Frontiers in Oncology, 13 1091379, 1091379. doi: 10.3389/fonc.2023.1091379
Yin, Xiaole, Chen, Xi, Jiang, Xiao-Tao, Yang, Ying, Li, Bing, Shum, Marcus Ho-Hin, Lam, Tommy T. Y., Leung, Gabriel M., Rose, Joan, Sanchez-Cid, Concepcion, Vogel, Timothy M., Walsh, Fiona, Berendonk, Thomas U., Midega, Janet, Uchea, Chibuzor, Frigon, Dominic, Wright, Gerard D., Bezuidenhout, Carlos, Picão, Renata C., Ahammad, Shaikh Z., Nielsen, Per Halkjær, Hugenholtz, Philip, Ashbolt, Nicholas J., Corno, Gianluca, Fatta-Kassinos, Despo, Bürgmann, Helmut, Schmitt, Heike, Cha, Chang-Jun, Pruden, Amy ... Zhang, Tong (2023). Toward a universal unit for quantification of antibiotic resistance genes in environmental samples. Environmental Science and Technology, 57 (26), 9713-9721. doi: 10.1021/acs.est.3c00159
McDonald, Daniel, Jiang, Yueyu, Balaban, Metin, Cantrell, Kalen, Zhu, Qiyun, Gonzalez, Antonio, Morton, James T., Nicolaou, Giorgia, Parks, Donovan H., Karst, Søren M., Albertsen, Mads, Hugenholtz, Philip, DeSantis, Todd, Song, Se Jin, Bartko, Andrew, Havulinna, Aki S., Jousilahti, Pekka, Cheng, Susan, Inouye, Michael, Niiranen, Teemu, Jain, Mohit, Salomaa, Veikko, Lahti, Leo, Mirarab, Siavash and Knight, Rob (2023). Author Correction: Greengenes2 unifies microbial data in a single reference tree (Nature Biotechnology, (2023), 10.1038/s41587-023-01845-1). Nature Biotechnology, 42 (5), 813-813. doi: 10.1038/s41587-023-02026-w
Budden, Kurtis F., Gellatly, Shaan L., Vaughan, Annalicia, Amorim, Nadia, Horvat, Jay C., Hansbro, Nicole G., Wood, David L. A., Hugenholtz, Philip, Dennis, Paul G., Wark, Peter A. B. and Hansbro, Philip M. (2022). Probiotic Bifidobacterium longum subsp. longum protects against cigarette smoke-induced inflammation in mice. International Journal of Molecular Sciences, 24 (1) 252, 1-12. doi: 10.3390/ijms24010252
Chaumeil, Pierre-Alain, Mussig, Aaron J., Hugenholtz, Philip and Parks, Donovan H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38 (23), 5315-5316. doi: 10.1093/bioinformatics/btac672
Hedlund, Brian P., Chuvochina, Maria, Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain C., Venter, Stephanus N. and Whitman, William B. (2022). SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nature Microbiology, 7 (10), 1702-1708. doi: 10.1038/s41564-022-01214-9
Montgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Ray, Angelique E. , Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2022). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient‐poor Antarctic soils. Environmental Microbiology, 24 (9), 4491-4491. doi: 10.1111/1462-2920.16191
Whitman, William B., Chuvochina, Maria, Hedlund, Brian P., Hugenholtz, Philip, Konstantinidis, Konstantinos T., Murray, Alison E., Palmer, Marike, Parks, Donovan H., Probst, Alexander J., Reysenbach, Anna-Louise, Rodriguez-R, Luis M., Rossello-Mora, Ramon, Sutcliffe, Iain and Venter, Stephanus N. (2022). Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Systematic and Applied Microbiology, 45 (5) 126305, 1-8. doi: 10.1016/j.syapm.2022.126305
Ray, Angelique E., Zaugg, Julian, Benaud, Nicole, Chelliah, Devan S., Bay, Sean, Wong, Hon Lun, Leung, Pok Man, Ji, Mukan, Terauds, Aleks, Montgomery, Kate, Greening, Chris, Cowan, Don A., Kong, Weidong, Williams, Timothy J., Hugenholtz, Philip and Ferrari, Belinda C. (2022). Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. The ISME Journal, 16 (11), 1-14. doi: 10.1038/s41396-022-01298-5
Hallstrøm, Søren, Raina, Jean-Baptiste, Ostrowski, Martin, Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip, Stocker, Roman, Seymour, Justin R. and Riemann, Lasse (2022). Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean. The ISME Journal, 16 (11), 2525-2534. doi: 10.1038/s41396-022-01299-4
Liu, Yongqin, Ji, Mukan, Yu, Tao, Zaugg, Julian, Anesio, Alexandre M., Zhang, Zhihao, Hu, Songnian, Hugenholtz, Philip, Liu, Keshao, Liu, Pengfei, Chen, Yuying, Luo, Yingfeng and Yao, Tandong (2022). A genome and gene catalog of glacier microbiomes. Nature Biotechnology, 40 (9), 1341-1348. doi: 10.1038/s41587-022-01367-2
Krueger, Annika, Mohamed, Ahmed, Kolka, Cathryn M., Stoll, Thomas, Zaugg, Julian, Linedale, Richard, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Frazer, Ian H. and Hill, Michelle M. (2022). Skin cancer-associated S. aureus strains can induce DNA damage in human keratinocytes by downregulating DNA repair and promoting oxidative stress. Cancers, 14 (9) 2143, 2143. doi: 10.3390/cancers14092143
Raina, Jean-Baptiste, Lambert, Bennett S., Parks, Donovan H., Rinke, Christian, Siboni, Nachshon, Bramucci, Anna, Ostrowski, Martin, Signal, Brandon, Lutz, Adrian, Mendis, Himasha, Rubino, Francesco, Fernandez, Vicente I., Stocker, Roman, Hugenholtz, Philip, Tyson, Gene W. and Seymour, Justin R. (2022). Chemotaxis shapes the microscale organization of the ocean’s microbiome. Nature, 605 (7908), 132-138. doi: 10.1038/s41586-022-04614-3
Krueger, Annika, Zaugg, Julian, Lachner, Nancy, Bialasiewicz, Seweryn, Lin, Lynlee L., Gabizon, Sharon, Sobarun, Priyamvada, Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip and Frazer, Ian H. (2022). Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients. ISME Communications, 2 (1) 13, 13. doi: 10.1038/s43705-022-00095-7
Krueger, Annika, Zaugg, Julian, Chisholm, Sarah, Linedale, Richard, Lachner, Nancy, Teoh, Siok Min, Tuong, Zewen K., Lukowski, Samuel W., Morrison, Mark, Soyer, H. Peter, Hugenholtz, Philip, Hill, Michelle M. and Frazer, Ian H. (2022). Secreted toxins from Staphylococcus aureus strains isolated from keratinocyte skin cancers mediate pro-tumorigenic inflammatory responses in the skin. Frontiers in Microbiology, 12 789042, 789042. doi: 10.3389/fmicb.2021.789042
Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2022). Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota. ISME Communications, 2 (1) 6, 6. doi: 10.1038/s43705-021-00048-6
Blyton, Michaela D. J., Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Characterization of the juvenile koala gut microbiome across wild populations. Environmental Microbiology, 24 (9), 4209-4219. doi: 10.1111/1462-2920.15884
Parks, Donovan H., Chuvochina, Maria, Rinke, Christian, Mussig, Aaron J., Chaumeil, Pierre-Alain and Hugenholtz, Philip (2022). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50 (D1), D785-D794. doi: 10.1093/nar/gkab776
Blyton, Michaela D.J, Soo, Rochelle M., Hugenholtz, Philip and Moore, Ben D. (2022). Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development. Environmental Microbiology, 24 (1), 475-493. doi: 10.1111/1462-2920.15858
Wang, Yulin, Ye, Jun, Ju, Feng, Liu, Lei, Boyd, Joel A., Deng, Yu, Parks, Donovan H., Jiang, Xiaotao, Yin, Xiaole, Woodcroft, Ben J., Tyson, Gene W., Hugenholtz, Philip, Polz, Martin F. and Zhang, Tong (2021). Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years. Microbiome, 9 (1) 199, 199. doi: 10.1186/s40168-021-01151-5
Bramucci, Anna R., Focardi, Amaranta, Rinke, Christian, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Raina, Jean-Baptiste (2021). Microvolume DNA extraction methods for microscale amplicon and metagenomic studies. ISME Communications, 1 (1) 79. doi: 10.1038/s43705-021-00079-z
Wilson, Liam A., Knaven, Esmée G., Morris, Marc T., Monteiro Pedroso, Marcelo, Schofield, Christopher J., Brück, Thomas, Boden, Mikael, Waite, David W., Hugenholtz, Philip, Guddat, Luke and Schenk, Gerhard (2021). Kinetic and structural characterization of the first B3 metallo-β-lactamase with an active site glutamic acid. Antimicrobial Agents and Chemotherapy, 65 (10) e00936-21, e0093621. doi: 10.1128/aac.00936-21
Bowerman, Kate L., Knowles, Sarah C. L., Bradley, Janette E., Baltrūnaitė, Laima, Lynch, Michael D. J., Jones, Kathryn M. and Hugenholtz, Philip (2021). Effects of laboratory domestication on the rodent gut microbiome. ISME Communications, 1 (1) 49, 49. doi: 10.1038/s43705-021-00053-9
Montgomery, Kate, Williams, Timothy J., Brettle, Merryn, Berengut, Jonathan F., Zhang, Eden, Zaugg, Julian, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Persistence and resistance: survival mechanisms of Candidatus Dormibacterota from nutrient-poor Antarctic soils. Environmental Microbiology, 23 (8), 4276-4294. doi: 10.1111/1462-2920.15610
Chiri, Eleonora, Nauer, Philipp A., Lappan, Rachael, Jirapanjawat, Thanavit, Waite, David W., Handley, Kim M., Hugenholtz, Philip, Cook, Perran L.M., Arndt, Stefan K. and Greening, Chris (2021). Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds. Proceedings of the National Academy of Sciences of the United States of America, 118 (30) e2102625118, 1-8. doi: 10.1073/pnas.2102625118
Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2021). Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications, 1 (1) 30, 1-14. doi: 10.1038/s43705-021-00032-0
Rinke, Christian, Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Davín, Adrián A., Waite, David W., Whitman, William B., Parks, Donovan H. and Hugenholtz, Philip (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology, 6 (7), 946-959. doi: 10.1038/s41564-021-00918-8
Nayfach, Stephen, Páez-Espino, David, Call, Lee, Low, Soo Jen, Sberro, Hila, Ivanova, Natalia N., Proal, Amy D., Fischbach, Michael A., Bhatt, Ami S., Hugenholtz, Philip and Kyrpides, Nikos C. (2021). Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nature Microbiology, 6 (7), 960-970. doi: 10.1038/s41564-021-00928-6
Bay, Sean K., Waite, David W., Dong, Xiyang, Gillor, Osnat, Chown, Steven L., Hugenholtz, Philip and Greening, Chris (2021). Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. The ISME Journal, 15 (11), 3339-3356. doi: 10.1038/s41396-021-01001-0
Coleman, Gareth A., Davín, Adrián A., Mahendrarajah, Tara A., Szánthó, Lénárd L., Spang, Anja, Hugenholtz, Philip, Szöllősi, Gergely J. and Williams, Tom A. (2021). A rooted phylogeny resolves early bacterial evolution. Science, 372 (6542) eabe0511, eabe0511-+. doi: 10.1126/science.abe0511
Pribyl, Alena L., Parks, Donovan H., Angel, Nicola Z., Boyd, Joel A., Hasson, Alexander G., Fang, Liang, MacDonald, Samantha L., Wills, Blake A., Wood, David L. A., Krause, Lutz, Tyson, Gene W. and Hugenholtz, Philip (2021). Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME Communications, 1 (1) 14, 14. doi: 10.1038/s43705-021-00014-2
Henden, Andrea S., Koyama, Motoko, Robb, Renee J., Forero, Adriana, Kuns, Rachel D., Chang, Karshing, Ensbey, Kathleen S., Varelias, Antiopi, Kazakoff, Stephen H., Waddell, Nicole, Clouston, Andrew D., Giri, Rabina, Begun, Jakob, Blazar, Bruce R., Degli-Esposti, Mariapia A., Kotenko, Sergei V., Lane, Steven W., Bowerman, Kate L., Savan, Ram, Hugenholtz, Philip, Gartlan, Kate H. and Hill, Geoffrey R. (2021). IFN-λ therapy prevents severe gastrointestinal graft-versus-host disease. Blood, 138 (8), 722-737. doi: 10.1182/blood.2020006375
Chen, Ya-Jou, Leung, Pok Man, Wood, Jennifer L., Bay, Sean K., Hugenholtz, Philip, Kessler, Adam J., Shelley, Guy, Waite, David W., Franks, Ashley E., Cook, Perran L. M. and Greening, Chris (2021). Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem. The ISME Journal, 15 (10), 2986-3004. doi: 10.1038/s41396-021-00988-w
Parks, Donovan H., Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W. and Wood, David L. A. (2021). Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome. Frontiers in Microbiology, 12 643682, 1-15. doi: 10.3389/fmicb.2021.643682
Hugenholtz, Philip, Chuvochina, Maria, Oren, Aharon, Parks, Donovan H. and Soo, Rochelle M. (2021). Prokaryotic taxonomy and nomenclature in the age of big sequence data. The ISME Journal, 15 (7), 1879-1892. doi: 10.1038/s41396-021-00941-x
Ji, Mukan, Williams, Timothy J., Montgomery, Kate, Wong, Hon Lun, Zaugg, Julian, Berengut, Jonathan F., Bissett, Andrew, Chuvochina, Maria, Hugenholtz, Philip and Ferrari, Belinda C. (2021). Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations. The ISME Journal, 15 (9), 2692-2707. doi: 10.1038/s41396-021-00944-8
Moentadj, Rabia, Wang, Yiwen, Bowerman, Kate, Rehaume, Linda, Nel, Hendrik, O Cuiv, Paraic, Stephens, Juliette, Baharom, Amalina, Maradana, Muralidhara, Lakis, Vanessa, Morrison, Mark, Wells, Timothy, Hugenholtz, Philip, Benham, Helen, Le Cao, Kim-Anh and Thomas, Ranjeny (2021). Streptococcus species enriched in the oral cavity of patients with RA are a source of peptidoglycan-polysaccharide polymers that can induce arthritis in mice. Annals of the Rheumatic Diseases, 80 (5) annrheumdis-2020-219009, annrheumdis-2020. doi: 10.1136/annrheumdis-2020-219009
Donner, Erica, Zamyadi, Arash, Jex, Aaron, Short, Michael, Drigo, Barbara, McCarthy, David, Crosbie, Nicholas, Ahmed, Warish, Mueller, Jochen, Thomas, Kevin, Monis, Paul, Keegan, Alex, Ginige, Maneesha, Hugenholtz, Philip, Tyson, Gene, Hill, Kelly and Blackall, Linda (2021). Wastewater monitoring for SARS-CoV-2. Microbiology Australia, 42 (1), 18-22. doi: 10.1071/ma21006
Campbell, B. C., Al Kouba, J., Timbrell, V., Noor, M. J., Massel, K., Gilding, E. K., Angel, N., Kemish, B., Hugenholtz, P., Godwin, I. D. and Davies, J. M. (2020). Tracking seasonal changes in diversity of pollen allergen exposure: targeted metabarcoding of a subtropical aerobiome. Science of the Total Environment, 747 141189, 141189. doi: 10.1016/j.scitotenv.2020.141189
Schriml, Lynn M., Chuvochina, Maria, Davies, Neil, Eloe-Fadrosh, Emiley A., Finn, Robert D., Hugenholtz, Philip, Hunter, Christopher I., Hurwitz, Bonnie L., Kyrpides, Nikos C., Meyer, Folker, Mizrachi, Ilene Karsch, Sansone, Susanna-Assunta, Sutton, Granger, Tighe, Scott and Walls, Ramona (2020). COVID-19 pandemic reveals the peril of ignoring metadata standards. Scientific Data, 7 (1) 188, 188. doi: 10.1038/s41597-020-0524-5
Bandara, H. M.H.N., Wood, D. L.A., Vanwonterghem, I., Hugenholtz, P., Cheung, B. P.K. and Samaranayake, L. P. (2020). Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing. Scientific Reports, 10 (1) 7769, 7769. doi: 10.1038/s41598-020-64761-3
Bowerman, Kate L., Rehman, Saima Firdous, Vaughan, Annalicia, Lachner, Nancy, Budden, Kurtis F., Kim, Richard Y., Wood, David L. A., Gellatly, Shaan L., Shukla, Shakti D., Wood, Lisa G., Yang, Ian A., Wark, Peter A., Hugenholtz, Philip and Hansbro, Philip M. (2020). Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease. Nature Communications, 11 (1) 5886, 1-15. doi: 10.1038/s41467-020-19701-0
Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S. G., Colman, Daniel R., DeAngelis, Kristen M. ... Reysenbach, Anna-Louise (2020). Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 6 (1), 136-136. doi: 10.1038/s41564-020-00827-2
Parks, Donovan H., Chuvochina, Maria, Chaumeil, Pierre-Alain, Rinke, Christian, Mussig, Aaron J. and Hugenholtz, Philip (2020). Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea (Nature Biotechnology, (2020), 38, 9, (1079-1086), 10.1038/s41587-020-0501-8). Nature Biotechnology, 38 (9), 1098-1098. doi: 10.1038/s41587-020-0539-7
Ahmed, Warish, Angel, Nicola, Edson, Janette, Bibby, Kyle, Bivins, Aaron, O'Brien, Jake W., Choi, Phil M., Kitajima, Masaaki, Simpson, Stuart L., Li, Jiaying, Tscharke, Ben, Verhagen, Rory, Smith, Wendy J.M., Zaugg, Julian, Dierens, Leanne, Hugenholtz, Philip, Thomas, Kevin V. and Mueller, Jochen F. (2020). First confirmed detection of SARS-CoV-2 in untreated wastewater in Australia: a proof of concept for the wastewater surveillance of COVID-19 in the community. Science of the Total Environment, 728 138764, 138764. doi: 10.1016/j.scitotenv.2020.138764
Almeida, Alexandre, Nayfach, Stephen, Boland, Miguel, Strozzi, Francesco, Beracochea, Martin, Shi, Zhou Jason, Pollard, Katherine S., Sakharova, Ekaterina, Parks, Donovan H., Hugenholtz, Philip, Segata, Nicola, Kyrpides, Nikos C. and Finn, Robert D. (2020). A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology, 39 (1), 105-114. doi: 10.1038/s41587-020-0603-3
Ahmed, Warish, Bertsch, Paul M., Angel, Nicola, Bibby, Kyle, Bivins, Aaron, Dierens, Leanne, Edson, Janette, Ehret, John, Gyawali, Pradip, Hamilton, Kerry, Hosegood, Ian, Hugenholtz, Philip, Jiang, Guangming, Kitajima, Masaaki, Sichani, Homa T., Shi, Jiahua, Shimko, Katja M., Simpson, Stuart L., Smith, Wendy J. M., Symonds, Erin M., Thomas, Kevin V., Verhagen, Rory, Zaugg, Julian and Mueller, Jochen F (2020). Detection of SARS-CoV-2 RNA in commercial passenger aircraft and cruise ship wastewater: a surveillance tool for assessing the presence of COVID-19 infected travelers. Journal of Travel Medicine, 27 (5) ARTN taaa116, 1-11. doi: 10.1093/jtm/taaa116
Pedroso, Marcelo Monteiro, Waite, David W., Melse, Okke, Wilson, Liam, Mitić, Nataša, McGeary, Ross P., Antes, Iris, Guddat, Luke W., Hugenholtz, Philip and Schenk, Gerhard (2020). Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse. Protein and Cell, 11 (8), 613-617. doi: 10.1007/s13238-020-00736-4
Parks, Donovan H., Chuvochina, Maria, Chaumeil, Pierre-Alain, Rinke, Christian, Mussig, Aaron J. and Hugenholtz, Philip (2020). A complete domain-to-species taxonomy for bacteria and archaea. Nature Biotechnology, 38 (9), 1098-1098. doi: 10.1038/s41587-020-0501-8
Carere, Carlo R., Steen, Jason A., Hugenholtz, Philip and Stott, Matthew B. (2020). Draft genome sequence of Limisphaera ngatamarikiensis NGM72.4(T), a moderately alkaliphilic thermophile belonging to the class Verrucomicrobiae. Microbiology Resource Announcements, 9 (18) e00225-20. doi: 10.1128/MRA.00225-20
Chaumeil, Pierre-Alain, Mussig, Aaron J., Hugenholtz, Philip and Parks, Donovan H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics, 36 (6), 1925-1927. doi: 10.1093/bioinformatics/btz848
Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2020). Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 14 (3), 878-878. doi: 10.1038/s41396-019-0556-z
Bowerman, Kate L., Varelias, Antiopi, Lachner, Nancy, Kuns, Rachel D., Hill, Geoffrey R. and Hugenholtz, Philip (2020). Continuous pre- and post-transplant exposure to a disease-associated gut microbiome promotes hyper-acute graft-versus-host disease in wild-type mice. Gut Microbes, 11 (4), 1-17. doi: 10.1080/19490976.2019.1705729
Murray, Alison E., Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos T., Lane, Christopher E., Papke, R. Thane, Parks, Donovan H., Rossello-Mora, Ramon, Stott, Matthew B., Sutcliffe, Iain C., Thrash, J. Cameron, Venter, Stephanus N., Whitman, William B., Acinas, Silvia G., Amann, Rudolf I., Anantharaman, Karthik, Armengaud, Jean, Baker, Brett J., Barco, Roman A., Bode, Helge B., Boyd, Eric S., Brady, Carrie L., Carini, Paul, Chain, Patrick S. G., Colman, Daniel R., DeAngelis, Kristen M. ... Reysenbach, Anna-Louise (2020). Roadmap for naming uncultivated Archaea and Bacteria. Nature Microbiology, 5 (8), 987-994. doi: 10.1038/s41564-020-0733-x
Waite, David W., Chuvochina, Maria, Pelikan, Claus, Parks, Donovan H., Yilmaz, Pelin, Wagner, Michael, Loy, Alexander, Naganuma, Takeshi, Nakai, Ryosuke, Whitman, William B., Hahn, Martin W., Kuever, Jan and Hugenholtz, Philip (2020). Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. International Journal of Systematic and Evolutionary Microbiology, 70 (11) 004213, 5972-6016. doi: 10.1099/ijsem.0.004213
Budden, Kurtis F., Shukla, Shakti D., Rehman, Saima Firdous, Bowerman, Kate L., Keely, Simon, Hugenholtz, Philip, Armstrong-James, Darius P. H., Adcock, Ian M., Chotirmall, Sanjay H., Chung, Kian Fan and Hansbro, Philip M. (2019). Functional effects of the microbiota in chronic respiratory disease. Lancet Respiratory Medicine, 7 (10), 907-920. doi: 10.1016/S2213-2600(18)30510-1
Whitman, William B., Klenk, Hans-Peter, Arahal, David R., Aznar, Rosa, Garrity, George, Pester, Michael and Hugenholtz, Philip (2019). Genomic Encyclopedia of Bacteria and Archaea (GEBA) VI: learning from type strains. Microbiology Australia, 40 (3), 125-129. doi: 10.1071/MA19034
Blyton, Michaela D. J., Soo, Rochelle M., Whisson, Desley, Marsh, Karen J., Pascoe, Jack, Le Pla, Mark, Foley, William, Hugenholtz, Philip and Moore, Ben D. (2019). Faecal inoculations alter the gastrointestinal microbiome and allow dietary expansion in a wild specialist herbivore, the koala. Animal Microbiome, 1 (1) 6, 6. doi: 10.1186/s42523-019-0008-0
Džunková, Mária, Low, Soo Jen, Daly, Joshua N., Deng, Li, Rinke, Christian and Hugenholtz, Philip (2019). Defining the human gut host–phage network through single-cell viral tagging. Nature Microbiology, 4 (12), 2192-2203. doi: 10.1038/s41564-019-0526-2
Low, Soo Jen, Džunková, Mária, Chaumeil, Pierre-Alain, Parks, Donovan H. and Hugenholtz, Philip (2019). Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales. Nature Microbiology, 4 (8), 1306-1315. doi: 10.1038/s41564-019-0448-z
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Consent insufficient for data release Response. Science, 364 (6439), 446-446. doi: 10.1126/science.aax7509
Kessler, Adam J., Chen, Ya-Jou, Waite, David W., Hutchinson, Tess, Koh, Sharlynn, Popa, M. Elena, Beardall, John, Hugenholtz, Philip, Cook, Perran L. M. and Greening, Chris (2019). Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments. Nature Microbiology, 4 (6), 1014-1023. doi: 10.1038/s41564-019-0391-z
Rehaume, Linda M., Matigian, Nicholas, Mehdi, Ahmed M., Lachner, Nancy, Bowerman, Kate L., Daly, Joshua, Lê Cao, Kim-Anh, Hugenholtz, Philip and Thomas, Ranjeny (2019). IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota. Annals of the Rheumatic Diseases, 78 (4), 494-503. doi: 10.1136/annrheumdis-2018-214381
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Toward unrestricted use of public genomic data. Science, 363 (6425), 350-352. doi: 10.1126/science.aaw1280
Evans, Paul N., Boyd, Joel A., Leu, Andy O., Woodcroft, Ben J., Parks, Donovan H., Hugenholtz, Philip and Tyson, Gene W. (2019). An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, 17 (4), 219-232. doi: 10.1038/s41579-018-0136-7
Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B. and Hugenholtz, Philip (2019). The importance of designating type material for uncultured taxa. Systematic and Applied Microbiology, 42 (1), 15-21. doi: 10.1016/j.syapm.2018.07.003
Soo, Rochelle M., Hemp, James and Hugenholtz, Philip (2019). Evolution of photosynthesis and aerobic respiration in the cyanobacteria. Free Radical Biology and Medicine, 140, 200-205. doi: 10.1016/j.freeradbiomed.2019.03.029
Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-Bum, Malmstrom, Rex R ... Eloe-Fadrosh, Emiley A (2018). Minimum information about an uncultivated virus genome (MIUViG). Nature Biotechnology, 37 (1), 29-37. doi: 10.1038/nbt.4306
Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2018). A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 13 (3), 663-675. doi: 10.1038/s41396-018-0282-y
Wood, David L. A., Lachner, Nancy, Tan, Jean-Marie, Tang, Stephanie, Angel, Nicola, Laino, Antonia, Linedale, Richard, Lê Cao, Kim-Anh, Morrison, Mark, Frazer, Ian H., Soyer, H. Peter and Hugenholtz, Philip (2018). A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes. MBio, 9 (5) e01432-18. doi: 10.1128/mBio.01432-18
Parks, Donovan H., Chuvochina, Maria, Waite, David W., Rinke, Christian, Skarshewski, Adam, Chaumeil, Pierre-Alain and Hugenholtz, Philip (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, 36 (10), 996-1004. doi: 10.1038/nbt.4229
Hoedt, Emily C., Parks, Donovan H., Volmer, James G., Rosewarne, Carly P., Denman, Stuart E., McSweeney, Christopher S., Muir, Jane G., Gibson, Peter R., Cuív, Páraic Ó, Hugenholtz, Philip, Tyson, Gene W. and Morrison, Mark (2018). Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME Journal, 12 (12), 2942-2953. doi: 10.1038/s41396-018-0225-7
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A, Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2018). Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893). Nature Biotechnology, 36 (7), 660-660. doi: 10.1038/nbt0718-660a
Waite, David W., Dsouza, Melissa, Sekiguchi, Yuji, Hugenholtz, Philip and Taylor, Michael W. (2018). Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo. Scientific Reports, 8 (1) 8128, 8128. doi: 10.1038/s41598-018-26484-4
Laloo, Andrew E., Wei, Justin, Wang, Dongbo, Narayanasamy, Shaman, Vanwonterghem, Inka, Waite, David, Steen, Jason, Kaysen, Anne, Heintz-Buschart, Anna, Wang, Qilin, Schulz, Benjamin, Nouwens, Amanda, Wilmes, Paul, Hugenholtz, Philip, Yuan, Zhiguo and Bond, Philip L. (2018). Mechanisms of persistence of the ammonia-oxidizing bacteria Nitrosomonas to the biocide free nitrous acid. Environmental science & technology, 52 (9), 5386-5397. doi: 10.1021/acs.est.7b04273
McDonald, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C., Dunn, Robert R., Fahimipour, Ashkaan K., Gaffney, James, Gilbert, Jack A., Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A., Janssen, Stefan, Jeste, Dilip V., Jiang, Lingjing, Kelley, Scott T., Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua ... Knight, Rob (2018). American gut: an open platform for citizen science microbiome research. mSystems, 3 (3) e00031-18. doi: 10.1128/mSystems.00031-18
Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H., Zhang, Ying, Takai, Ken, Sievert, Stefan M., Simon, Jorg, Campbell, Barbara J., Hanson, Thomas E., Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2018). Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017). Frontiers in Microbiology, 9 (APR) 772, 772. doi: 10.3389/fmicb.2018.00772
Varelias, Antiopi, Bunting, Mark D., Ormerod, Kate L., Koyama, Motoko, Olver, Stuart D., Straube, Jasmin, Kuns, Rachel D., Robb, Renee J., Henden, Andrea S., Cooper, Leanne, Lachner, Nancy, Gartlan, Kate H., Lantz, Olivier, Kjer-Nielsen, Lars, Mak, Jeffrey Y. W., Fairlie, David P., Clouston, Andrew D., McCluskey, James, Rossjohn, Jamie, Lane, Steven W., Hugenholtz, Philip and Hill, Geoffrey R. (2018). Recipient mucosal-associated invariant T cells control GVHD within the colon. Journal of Clinical Investigation, 128 (5), 1919-1936. doi: 10.1172/JCI91646
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Goeker, Markus, Coates, R. Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2018). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life (vol 35, pg 676, 2017). Nature Biotechnology, 36 (4), 368-368. doi: 10.1038/nbt0418-368c
Schofield, Benjamin J., Lachner, Nancy, Le, Oanh T., McNeill, David M., Dart, Peter, Ouwerkerk, Diane, Hugenholtz, Philip and Klieve, Athol V. (2018). Beneficial changes in rumen bacterial community profile in sheep and dairy calves as a result of feeding the probiotic Bacillus amyloliquefaciens H57. Journal of Applied Microbiology, 124 (3), 855-866. doi: 10.1111/jam.13688
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 3 (2), 253-253. doi: 10.1038/s41564-017-0083-5
Ji, Mukan, Greening, Chris, Vanwonterghem, Inka, Carere, Carlo R., Bay, Sean K., Steen, Jason A., Montgomery, Kate, Lines, Thomas, Beardall, John, van Dorst, Josie, Snape, Ian, Stott, Matthew B., Hugenholtz, Philip and Ferrari, Belinda C. (2017). Atmospheric trace gases support primary production in Antarctic desert surface soil. Nature, 552 (7685), 400-403. doi: 10.1038/nature25014
Yeoh, Yun Kit, Dennis, Paul G., Paungfoo-Lonhienne, Chanyarat, Weber, Lui, Brackin, Richard, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2017). Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence. Nature Communications, 8 (1) 002628, 215. doi: 10.1038/s41467-017-00262-8
Shiffman, Miriam E, Soo, Rochelle M, Dennis, Paul G, Morrison, Mark, Tyson, Gene W and Hugenholtz, Philip (2017). Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ, 5, 1-32. doi: 10.7717/peerj.4075
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 2 (11), 1533-1542. doi: 10.1038/s41564-017-0012-7
Lambert, Bennett S., Raina, Jean-Baptiste, Fernandez, Vicente I., Rinke, Christian, Siboni, Nachshon, Rubino, Francesco, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Stocker, Roman (2017). A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nature Microbiology, 2 (10), 1344-1349. doi: 10.1038/s41564-017-0010-9
Pedroso, Marcelo Monteiro, Selleck, Christopher, Enculescu, Charmaine, Harmer, Jeffrey R., Mitic, Natasa, Craig, Whitney R., Helweh, Waleed, Hugenholtz, Philip, Tyson, Gene W., Tierney, David L., Larrabee, James A. and Schenk, Gerhard (2017). Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics, 9 (8), 1157-1168. doi: 10.1039/c7mt00195a
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology, 35 (8), 725-731. doi: 10.1038/nbt.3893
Mukherjee, Supratim, Seshadri, Rekha, Varghese, Neha J., Eloe-Fadrosh, Emiley A., Meier-Kolthoff, Jan P., Göker, Markus, Coates, R Cameron, Hadjithomas, Michalis, Pavlopoulos, Georgios A., Paez-Espino, David, Yoshikuni, Yasuo, Visel, Axel, Whitman, William B., Garrity, George M., Eisen, Jonathan A., Hugenholtz, Philip, Pati, Amrita, Ivanova, Natalia N., Woyke, Tanja, Klenk, Hans-Peter and Kyrpides, Nikos C. (2017). 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.. Nature Biotechnology, 35 (7), 676-683. doi: 10.1038/nbt.3886
Bissett, Andrew, Fitzgerald, Anna, Court, Leon, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I. ... Young, Andrew (2017). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database (vol 5, 1, 2016). Gigascience, 6 (5) gix021, 1-1. doi: 10.1093/gigascience/gix021
Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H. , Zhang, Ying, Takai, Ken, Sievert, Stefan M. , Simon, Joerg, Campbell, Barbara J. , Hanson, Thomas E. , Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2017). Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology, 8 (APR) 682 doi: 10.3389/fmicb.2017.00682.
Soo, Rochelle M. , Hemp, James, Parks, Donovan H. , Fischer, Woodward W. and Hugenholtz, Philip (2017). On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. Science, 355 (6332), 1436-1440. doi: 10.1126/science.aal3794
Chotirmall, Sanjay H., Gellatly, Shaan L., Budden, Kurtis F., Mac Aogain, Micheál, Shukla, Shakti D., Wood, David L. A., Hugenholtz, Philip, Pethe, Kevin and Hansbro, Philip M. (2017). Microbiomes in respiratory health and disease: an Asia-Pacific perspective. Respirology, 22 (2), 240-250. doi: 10.1111/resp.12971
Varelias, Antiopi, Ormerod, Kate L., Bunting, Mark D., Koyama, Motoko, Gartlan, Kate H., Kuns, Rachel D., Lachner, Nancy, Locke, Kelly R., Lim, Chun Y., Henden, Andrea S., Zhang, Ping, Clouston, Andrew D., Hasnain, Sumaira Z., McGuckin, Michael A., Blazar, Bruce R., MacDonald, Kelli P. A ., Hugenholtz, Philip and Hill, Geoffrey R. (2017). Acute graft-versus-host disease is regulated by an IL-17-sensitive microbiome. Blood, 129 (15), 2172-2185. doi: 10.1182/blood-2016-08-732628
Dennis, Paul G., Virdis, Bernardino, Vanwonterghem, Inka, Hassan, Alif, Hugenholtz, Phil, Tyson, Gene W. and Rabaey, Korneel (2016). Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes. Scientific Reports, 6 (1) 39114, 39114. doi: 10.1038/srep39114
Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Donose, Bogdan C., Webb, Richard I., Parsons, Jeremy, Liao, Webber, Sagulenko, Evgeny, Lakshmanan, Prakash, Hugenholtz, Philip, Schmidt, Susanne and Ragan, Mark A. (2016). Crosstalk between sugarcane and a plant-growth promoting Burkholderia species. Scientific Reports, 6 (1) 37389, 37389. doi: 10.1038/srep37389
Budden, Kurtis F. , Gellatly, Shaan L. , Wood, David L., Cooper, Matthew A. , Morrison, Mark, Hugenholtz, Philip and Hansbro, Philip M. (2016). Emerging pathogenic links between microbiota and the gut-lung axis.. Nature Reviews Microbiology, 15 (1), 55-63. doi: 10.1038/nrmicro.2016.142
Vanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip and Tyson, Gene W. (2016). Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1 (16170) 16170, 16170. doi: 10.1038/nmicrobiol.2016.170
Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptista, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W. and Hugenholtz, Philip (2016). Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4 (9) e2486, 1-28. doi: 10.7717/peerj.2486
Schofield, Benjamin J., Skarshewski, Adam, Lachner, Nancy, Ouwerkerk, Diane, Klieve, Athol V., Dart, Peter and Hugenholtz, Philip (2016). Near complete genome sequence of the animal feed probiotic, Bacillus amyloliquefaciens H57. Standards in Genomic Sciences, 11 (1) 60, 60. doi: 10.1186/s40793-016-0189-z
Ikeda-Ohtsubo, Wakako, Strassert, Juergen F. H., Kohler, Tim, Mikaelyan, Aram, Gregor, Ivan, Mchardy, Alice C., Tringe, Susannah Green, Hugenholtz, Phil, Radek, Renate and Brune, Andreas (2016). 'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen. Environmental Microbiology, 18 (8), 2548-2564. doi: 10.1111/1462-2920.13234
Ormerod, Kate L., Wood, David L. A., Lachner, Nancy, Gellatly, Shaan L., Daly, Joshua N., Parsons, Jeremy D., Dal’Molin, Cristiana G. O., Palfreyman, Robin W., Nielsen, Lars K., Cooper, Matthew A., Morrison, Mark, Hansbro, Philip M. and Hugenholtz, Philip (2016). Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals. Microbiome, 4 (1) 36, 36.1-36.17. doi: 10.1186/s40168-016-0181-2
Haroon, Mohamed F., Thompson, Luke R., Parks, Donovan H., Hugenholtz, Philip and Stingl, Ulrich (2016). A catalogue of 136 microbial draft genomes from Red Sea metagenomes. Scientific Data, 3 (1) 160050, 160050.1-160050.6. doi: 10.1038/sdata.2016.50
Bissett, Andrew, Fitzgerald, Anna, Meintjes, Thys, Mele, Pauline M., Reith, Frank, Dennis, Paul G., Breed, Martin F., Brown, Belinda, Brown, Mark V., Brugger, Joel, Byrne, Margaret, Caddy-Retalic, Stefan, Carmody, Bernie, Coates, David J., Correa, Carolina, Ferrari, Belinda C., Gupta, Vadakattu V. S. R., Hamonts, Kelly, Haslem, Asha, Hugenholtz, Philip, Karan, Mirko, Koval, Jason, Lowe, Andrew J., Macdonald, Stuart, McGrath, Leanne, Martin, David, Morgan, Matt, North, Kristin I., Paungfoo-Lonhienne, Chanyarat ... Young, Andrew (2016). Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database. Gigascience, 5 (1) 21, 21.1-21.11. doi: 10.1186/s13742-016-0126-5
Hugenholtz, Philip, Skarshewski, Adam and Parks, Donovan H. (2016). Genome-based microbial taxonomy coming of age. Cold Spring Harbor Perspectives in Biology, 8 (6) a018085, a018085. doi: 10.1101/cshperspect.a018085
Simpson, Jodie L., Daly, Joshua, Baines, Katherine J., Yang, Ian A., Upham, John W., Reynolds, Paul N., Hodge, Sandra, James, Alan L., Hugenholtz, Philip, Willner, Dana and Gibson, Peter G. (2016). Airway dysbiosis: Haemophilus influenzae and Tropheryma in poorly controlled asthma. European Respiratory Journal, 47 (3), 792-800. doi: 10.1183/13993003.00405-2015
Vavourakis, Charlotte D., Ghai, Rohit, Rodriguez-Valera, Francisco, Sorokin, Dimitry Y., Tringe, Susannah G., Hugenholtz, Philip and Muyzer, Gerard (2016). Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines. Frontiers in Microbiology, 7 (FEB) 211, 211.1-211.18. doi: 10.3389/fmicb.2016.00211
Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan-Fang, Copeland, Alex, Klenk, Hans-Peter, Hallam, Steven J., Hugenholtz, Philip, Tringe, Susannah G. and Woyke, Tanja (2016). High-resolution phylogenetic microbial community profiling. ISME Journal, 10 (8), 2020-2032. doi: 10.1038/ismej.2015.249
Abdul Rahman, Nurdyana, Parks, Donovan H., Vanwonterghem, Inka, Morrison, Mark, Tyson, Gene W. and Hugenholtz, Philip (2016). A phylogenomic analysis of the bacterial phylum fibrobacteres. Frontiers in Microbiology, 6 (JAN) 1469, 1469.1-1469.15. doi: 10.3389/fmicb.2015.01469
Yeoh, Yun Kit, Sekiguchi, Yuji, Parks, Donovan H. and Hugenholtz, Philip (2015). Comparative genomics of candidate phylum TM6 suggests that parasitism is widespread and ancestral in this lineage. Molecular Biology and Evolution, 33 (4), 915-927. doi: 10.1093/molbev/msv281
Lu, Yang, Hugenholtz, Phillip and Batstone, Damien John (2015). Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community. PLoS One, 10 (11) e0142720, e0142720.1-e0142720.10. doi: 10.1371/journal.pone.0142720
Matsuura, Norihisa, Tourlousse, Dieter M., Ohashi, Akiko, Hugenholtz, Philip and Sekiguchia, Yuji (2015). Draft genome sequences of Anaerolinea thermolimosa IMO-1, Bellilinea caldifistulae GOMI-1, Leptolinea tardivitalis YMTK-2, Levilinea saccharolytica KIBI-1, Longilinea arvoryzae KOME-1, previously described as members of the class Anaerolineae (Chloroflexi. Genome Announcements, 3 (5) e00975-15. doi: 10.1128/genomeA.00975-15
Ormerod, Kate L., George, Narelle M., Fraser, James A., Wainwright, Claire and Hugenholtz, Philip (2015). Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients. PeerJ, 3 (9) e1223, e1223.1-e1223.27. doi: 10.7717/peerj.1223
Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25 (7), 1043-1055. doi: 10.1101/gr.186072.114
Leong, Lex E. X., Denman, Stuart E., Hugenholtz, Philip and McSweeney, Christopher S. (2015). Amino acid and peptide utilization profiles of the fluoroacetate-degrading bacterium synergistetes strain MFA1 under varying conditions. Microbial Ecology, 71 (2), 494-504. doi: 10.1007/s00248-015-0641-4
Yeoh, Yun Kit, Paungfoo-Lonhienne, Chanyarat, Dennis, Paul G., Robinson, Nicole, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2015). The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application.. Environmental Microbiology, 18 (5), 1338-1351. doi: 10.1111/1462-2920.12925
Whitman, William B., Woyke, Tanja, Klenk, Hans-Peter, Zhou, Yuguamg, Lilburn, Timothy G., Beck, Brian J., De Vos, Paul, Vandamme, Peter, Eisen, Jonathan A., Garrity, George, Hugenholtz, Philip and Kyrpides, Nikos C. (2015). Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains. Standards in Genomic Sciences, 10 (26) 26, 26. doi: 10.1186/s40793-015-0017-x
Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy A., Schembri, Mark A., Tyson, Gene W. and Hugenholtz, Philip (2015). Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome. Journal of Microbiology and Biology Education, 16 (1), 50-60. doi: 10.1128/jmbe.v16i1.816
Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2015). Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.. PeerJ, 2015 (5) e968, Art. No.: e968-Art. No.: e968. doi: 10.7717/peerj.968
Paungfoo-Lonhienne, Chanyarat, Yeoh, Yun Kit, Kasinadhuni, Naga Rup Pinaki, Lonhienne, Thierry G. A., Robinson, Nicole, Hugenholtz, Philip, Ragan, Mark A. and Schmidt, Susanne (2015). Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere.. Scientific Reports, 5 (8678) 8678, 1-6. doi: 10.1038/srep08678
Abdul Rahman, Nurdyana, Parks, Donovan H., Willner, Dana L., Engelbrektson, Anna L., Goffredi, Shana K., Warnecke, Falk, Scheffrahn, Rudolf H. and Hugenholtz, Philip (2015). A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome, 3 (5) 5, 1-16. doi: 10.1186/s40168-015-0067-8
Sekiguchi, Yuji, Ohashi, Akiko, Parks, Donovan H., Yamauchi, Toshihiro, Tyson, Gene W. and Hugenholtz, Philip (2015). First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ, 3 (e740) e740, 1-24. doi: 10.7717/peerj.740
Scheuner, Carmen, Tindall, Brian J., Lu, Megan, Nolan, Matt, Lapidus, Alla, Cheng, Jan-Fang, Goodwin, Lynne, Pitluck, Sam, Huntemann, Marcel, Liolios, Konstantinos, Pagani, Ioanna, Mavromatis, Konstantinos, Ivanova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Jeffries, Cynthia D., Hauser, Loren, Land, Miriam, Mwirichia, Romano, Rohde, Manfred, Abt, Birte, Detter, John C., Woyke, Tanja, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Goker, Markus, Kyrpides, Nikos C. and Klenk, Hans-Peter (2014). Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Standards in Genomic Sciences, 9 (1) 10, 10. doi: 10.1186/1944-3277-9-10
Chambers, Daniel C., Gellatly, Shaan L., Hugenholtz, Philip and Hansbro, Philip M. (2014). JTD special edition 'Hot Topics in COPD'- the microbiome in COPD. Journal of Thoracic Disease, 6 (11), 1525-1531. doi: 10.3978/j.issn.2072-1439.2014.11.08
Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip and Tyson, Gene W. (2014). GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2014 (1) e603, 1-16. doi: 10.7717/peerj.603
Kyrpides, Nikos C., Hugenholtz, Philip, Eisen, Jonathan A., Woyke, Tanja, Goker, Markus, Parker, Charles T., Amann, Rudolf, Beck, Brian J., Chun, Jongsik, Colwell, Rita R., Danchin, Antoine, Dawyndt, Peter, Dedeurwaerdere, Tom, DeLong, Edward F., Detter, John C., De Vos, Paul, Donohue, Timothy J., Dong, Xiu-Zhu, Ehrlich, Dusko S., Fraser, Claire, Gibbs, Richard, Gilbert, Jack, Gilna, Paul, Glockner, Frank Oliver, Jansson, Janet K., Keasling, Jay D., Knight, Rob, Labeda, David, Lapidus, Alla ... Klenk, Hans-Peter (2014). Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biology, 12 (8) e1001920, e1001920.1-e1001920.7. doi: 10.1371/journal.pbio.1001920
Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip and Beiko, Robert G. (2014). STAMP: Statistical analysis of taxonomic and functional profiles.. Bioinformatics., 30 (21), 3123-3124. doi: 10.1093/bioinformatics/btu494
Vanwonterghem, Inka, Jensen, Paul D., Dennis, Paul G., Hugenholtz, Philip, Rabaey, Korneel and Tyson, Gene W. (2014). Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME Journal, Advance Online (10), 1-14. doi: 10.1038/ismej.2014.50
Soo, Rochelle M., Skennerton, Connor T., Sekiguchi, Yuji, Imelfort, Michael, Paech, Samuel J., Dennis, Paul G., Steen, Jason A., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2014). An expanded genomic representation of the phylum Cyanobacteria. Genome Biology and Evolution, Advance Access (5), 1-42. doi: 10.1093/gbe/evu073
Angly, Florent E., Dennis, Paul G., Skarshewski, Adam, Vanwonterghem, Inka, Hugenholtz, Philip and Tyson, Gene W. (2014). CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome, 2 (11) 11, 11. doi: 10.1186/2049-2618-2-11
Paungfoo-Lonhienne, Chanyarat, Lonhienne, Thierry G. A., Yeoh, Yun Kit, Webb, Richard I., Lakshmanan, Prakash, Chan, Cheong Xin, Lim, Phaik-Eem, Ragan, Mark A., Schmidt, Susanne and Hugenholtz, Philip (2014). A new species of Burkholderia isolated from sugarcane roots promotes plant growth. Microbial Biotechnology, 7 (2), 142-154. doi: 10.1111/1751-7915.12105
Willner, Dana, Low, Serene, Steen, Jason A., George, Narelle, Nimmo, Graeme R., Schembri, Mark A. and Hugenholtz, Philip (2014). Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant In Situ populations. mBio, 5 (2) e01064-13, e01064-13.1-e01064-13.10. doi: 10.1128/mBio.01064-13
Mondav, Rhiannon, Woodcroft, Ben J., Kim, Eun-Hae, McCalley, Carmody K., Hodgkins, Suzanne B., Crill, Patrick M., Chanton, Jeffrey, Hurst, Gregory B., VerBerkmoes, Nathan C., Saleska, Scott R., Hugenholtz, Philip, Rich, Virginia I. and Tyson, Gene W. (2014). Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5 (1) 3212, 3212.1-3212.7. doi: 10.1038/ncomms4212
Göker, Markus, Spring, Stefan, Scheuner, Carmen, Anderson, Iain, Zeytun, Ahmet, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-juan, Jeffries, Cynthia D., Rohde, Manfred, Detter, John C., Woyke, Tanja ... Lapidus, Alla (2014). Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring. Standards in Genomic Sciences, 9 (3), 1105-1117. doi: 10.4056/sigs.3016383
Goeker, Markus, Lu, Megan, Fiebig, Anne, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina Del Rio, Tijana, Cheng, Jan-Feng, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Mayilraj, Shanmugam, Rohde, Manfred, Detter, John C., Bunk, Boyke, Spring, Stefan, Wirth, Reinhard, Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2014). Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 (T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Standards in Genomic Sciences, 9 (3), 1076-1088. doi: 10.4056/sigs.5138968
Clingenpeel, Scott, Schwientek, Patrick, Hugenholtz, Philip and Woyke, Tanja (2014). Effects of sample treatments on genome recovery via single-cell genomics. The ISME Journal, 8 (12), 2546-2549. doi: 10.1038/ismej.2014.92
Lonhienne, Thierry, Mason, Michael G., Ragan, Mark A., Hugenholtz, Philip, Schmidt, Susanne and Paungfoo-Lonhienne, Chanyarat (2014). Yeast as a biofertilizer alters plant growth and morphology. Crop Science, 54 (2), 785-790. doi: 10.2135/cropsci2013.07.0488
Deng, Li, Ignacio-Espinoza, J. Cesar, Gregory, Ann C., Poulos, Bonnie T., Weitz, Joshua S., Hugenholtz, Philip and Sullivan, Matthe B. (2014). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.. Nature, 513 (7517), 242-245 + 13. doi: 10.1038/nature13459
Vipin Madhavan, T. P., Steen, Jason A., Hugenholtz, Philip and Sakellaris, Harry (2014). Genome sequence of enterotoxigenic Escherichia coli strain B2C. Genome Announcements, 2 (2) e00247-14. doi: 10.1128/genomeA.00247-14
Braff, William A., Willner, Dana, Hugenholtz, Philip, Rabaey, Korneel and Buie, Cullen R. (2013). Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties. PLoS ONE, 8 (1) e76751, e76751.1-e76751.7. doi: 10.1371/journal.pone.0076751
Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 501 (7468), 578-578. doi: 10.1038/nature12619
Lundberg, Derek S., Lebeis, Sarah L., Paredes, Sur Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna, Kunin, Victor, Del Rio, Tijana Glavina, Edgar, Robert C., Eickhorst, Thilo, Ley, Ruth E., Hugenholtz, Philip, Tringe, Susannah Green and Dangl, Jeffery L. (2013). Defining the core Arabidopsis thaliana root microbiome. Nature, 501 (7468 SUPPL.).
Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip and Woyke, Tanja (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499 (7459), 431-437. doi: 10.1038/nature12352
D'haeseleer, Patrik, Gladden, John M., Allgaier, Martin, Chain, Patrik S. G., Tringe, Susannah G., Malfatti, Stephanie A., Aldrich, Joshua T., Nicora, Carrie D., Robinson, Errol W., Pasa-Tolic, Ljiljana, Hugenholtz, Philip, Simmons, Blake A. and Singer, Steven W. (2013). Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. Plos One, 8 (7) e68465, e68465.1-e68465.11. doi: 10.1371/journal.pone.0068465
Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 (6), 533-538+. doi: 10.1038/nbt.2579
Willner, Dana and Hugenholtz, Philip (2013). From deep sequencing to viral tagging: recent advances in viral metagenomics. Bioessays, 35 (5), 436-442. doi: 10.1002/bies.201200174
He, Shaomei, Ivanova, Natalia, Kirton, Edward, Allgaier, Martin, Bergin, Claudia, Scheffrahn, Rudolf H., Kyrpides, Nikos C., Warnecke, Falk, Tringe, Susannah G. and Hugenholtz, Philip (2013). Comparative metagenomic and metatranscriptomic analysis of hindgut paunch microbiota in wood- and dung-feeding higher termites. PLoS One, 8 (4) e61126, e61126. doi: 10.1371/journal.pone.0061126
Bragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip and Tyson, Gene W. (2013). Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. Plos Computational Biology, 9 (4) e1003031, e1003031.1-e1003031.18. doi: 10.1371/journal.pcbi.1003031
Deng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2013). Contrasting Life Strategies of Viruses That Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging (vol 3, e00373, 2012). Mbio, 4 (1). doi: 10.1128/mBio.00516-12
Kyrpides, Nikos C., Woyke, Tanja, Eisen, Jonathan A., Garrity, George, Lilburn, Timothy G., Beck, Brian J., Whitman, William B., Hugenholtz, Phil and Klenk, Hans-Peter (2013). Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project. Standards in Genomic Sciences, 9 (3), 628-634. doi: 10.4056/sigs.5068949
Anderson, Iain, Teshima, Huzuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Lang, Elke, Detter, John C., Goker, Markus, Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Klenk, Hans-Peter (2013). Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl. Standards in Genomic Sciences, 9 (1), 83-92. doi: 10.4056/sigs.4338002
Palaniappan, Krishna, Meier-Kolthoff, Jan P., Teshima, Hazuki, Nolan, Matt, Lapidus, Alla, Tice, Hope, Glavina del Rio, Tijana, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Rohde, Manfred, Mayilraj, Shanmugam, Spring, Stefan, Detter, John C., Goker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C. ... Woyke, Tanja (2013). Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701T) and emended description of the genus Thermanaerovibrio. Standards in Genomic Sciences, 9 (1), 57-70. doi: 10.4056/sigs.4237901
Garrity, George M., Banfield, Jill, Eisen, Jonathan, van der Lelie, Niels, McMahon, Trina, Rusch, Doug, Delong, Edward, Moran, Mary Ann, Currie, Cameron, Furhman, Jed, Hallam, Steve, Hugenholtz, Phil, Moran, Nancy, Nelson, Karen, Roberts, Richard and Stepanauskas, Ramunas (2013). Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2013. Standards in Genomic Sciences, 8 (3), 561-570. doi: 10.4056/sigs.4638348
Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Klenk, Hans-Peter (2013). Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H-T), and emendation of the species Turneriella parva. Standards in Genomic Sciences, 8 (2), 228-238. doi: 10.4056/sigs.3617113
Liolos, Konstantinos, Abt, Birte, Scheuner, Carmen, Teshima, Hazuki, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Detter, John C., Goeker, Markus, Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Kyrpides, Nikos C. (2013). Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. Standards in Genomic Sciences, 8 (2), 165-176. doi: 10.4056/sigs.3607108
Huntemann, Marcel, Stackebrandt, Erko, Held, Brittany, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Woyke, Tanja, Hugenholtz, Philip ... Lapidus, Alla (2013). Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). Standards in Genomic Sciences, 8 (2), 177-187. doi: 10.4056/sigs.3637201
Mavromatis, Konstantinos, Stackebrandt, Erko, Held, Brittany, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Spring, Stefan, Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Kyrpides, Nikos C. (2013). Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). Standards in Genomic Sciences, 8 (1), 47-57. doi: 10.4056/sigs.3547050
Mavromatis, Konstantinos, Stackebrandt, Erko, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Rohde, Manfred, Gronow, Sabine, Goeker, Markus, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor ... Woyke, Tanja (2013). Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)). Standards in Genomic Sciences, 8 (1), 26-36. doi: 10.4056/sigs.3527032
Abt, Birte, Goeker, Markus, Scheuner, Carmen, Han, Cliff, Lu, Megan, Misra, Monica, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Jeffries, Cynthia D., Rohde, Manfred, Spring, Stefan ... Klenk, Hans-Peter (2013). Genome sequence of the thermophilic fresh-water bacterium Spirochaeta caldaria type strain (H1(T)), reclassification of Spirochaeta caldaria, Spirochaeta stenostrepta, and Spirochaeta zuelzerae in the genus Treponema as Treponema caldaria comb. nov., Trep. Standards in Genomic Sciences, 8 (1), 88-105. doi: 10.4056/sigs.3096473
Stackebrandt, Erko, Zeytun, Ahmet, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Chang, Yun-juan, Land, Miriam, Hauser, Loren, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James ... Klenk, Hans-Peter (2013). Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). Standards in Genomic Sciences, 8 (1), 15-25. doi: 10.4056/sigs.3507020
Stackebrandt, Erko, Chertkov, Olga, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Han, Cliff, Cheng, Jan-Fang, Tapia, Roxanne, Goodwin, Lynne A., Bruce, David, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Woyke, Tanja, Detter, John C., Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Kyrpides, Nikos C. (2013). High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). Standards in Genomic Sciences, 8 (1), 37-46. doi: 10.4056/sigs.3537045
Flowers, Jason J., He, Shaomei, Malfatti, Stephanie, Glavina del Rio, Tijana, Tringe, Susannah G., Hugenholtz, Philip and McMahon, Katherine D. (2013). Comparative genomics of two 'Candidatus Accumulibacter' clades performing biological phosphorus removal. ISME Journal, 7 (12), 2301-2314. doi: 10.1038/ismej.2013.117
Willner, Dana and Hugenholtz, Phil (2013). Metagenomics and community profiling: culture-independent techniques in the clinical laboratory. Clinical Microbiology Newsletter, 35 (1), 1-9. doi: 10.1016/j.clinmicnews.2012.12.001
Willner, Dana L., Hugenholtz, Philip, Yerkovich, Stephanie T., Tan, Maxine E., Daly, Joshua N., Lachner, Nancy, Hopkins, Peter M. and Chambers, Daniel C. (2013). Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome. American Journal of Respiratory and Critical Care Medicine, 187 (6), 640-647. doi: 10.1164/rccm.201209-1680OC
Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500 (7464), 567-570. doi: 10.1038/nature12375
Haroon, Mohamed F., Skennerton, Connor T., Steen, Jason A., Lachner, Nancy, Hugenholtz, Philip and Tyson, Gene W. (2013). In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology, 531, 3-19. doi: 10.1016/B978-0-12-407863-5.00001-0
Harris, J. Kirk, Caporaso, J. Gregory, Walker, Jeffrey J., Spear, John R., Gold, Nicholas J., Robertson, Charles E., Hugenholtz, Philip, Goodrich, Julia, McDonald, Daniel, Knights, Dan, Marshall, Paul, Tufo, Henry, Knight, Rob and Pace, Norman R. (2013). Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat. ISME Journal, 7 (1), 50-60. doi: 10.1038/ismej.2012.79
Chappell, K.J., Brealey, J.C., Mackay, I.M., Bletchly, C., Hugenholtz, P., Sloots, T.P., Sly, P.D. and Young, P.R. (2013). Respiratory syncytial virus infection is associated with increased bacterial load in the upper respiratory tract in young children. Journal of Medical Microbiology & Diagnosis, S (1), 1-9. doi: 10.4172/2161-0703.S1-005
Anderson, Iain, Munk, Christine, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Tice, Hope, Del Rio, Tijana Glavina, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne, Pitluck, Sam, Liolios, Konstantinos, Mavromatis, Konstantinos, Pagani, Ioanna, Mikhailova, Natalia, Pati, Amrita, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Rohde, Manfred, Tindall, Brian J., Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A., Markowitz, Victor, Hugenholtz, Philip ... Ivanova, Natalia (2012). Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). Standards in Genomic Sciences, 7 (2), 210-220. doi: 10.4056/sigs.3117229
Deng, Li, Gregory, Ann, Yilmaz, Suzan, Poulos, Bonnie T., Hugenholtz, Philip and Sullivan, Matthew B. (2012). Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging. Mbio, 3 (6) e00373-12. doi: 10.1128/mBio.00373-12
Hugenholtz, Phil (2012). Guest commentary: the human microbiome and the promise of clinical ecology. Microbiology Australia, 33 (3), 90-90.
Lundberg, Derek S., Lebeis, Sarah L., Paredes, Sut Herrera, Yourstone, Scott, Gehring, Jase, Malfatti, Stephanie, Tremblay, Julien, Engelbrektson, Anna, Kunin, Victor, del Rio, Tijana Glavina, Edgar, Robert C., Eickhorst, Thilo, Ley, Ruth E., Hugenholtz, Philip, Tringe, Susannah Green and Dangl, Jeffery L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488 (7409), 86-90. doi: 10.1038/nature11237
Anderson, Iain, Chertkov, Olga, Chen, Amy, Saunders, Elizabeth, Lapidus, Alla, Nolan, Matt, Lucas, Susan, Hammon, Nancy, Deshpande, Shweta, Cheng, Jan-Fang, Han, Cliff, Tapia, Roxanne, Goodwin, Lynne A., Pitluck, Sam, Liolios, Konstantinos, Pagani, Ioanna, Ivanova, Natalia, Mikhailova, Natalia, Pati, Amrita, Palaniappan, Krishna, Land, Miriam, Pan, Chongle, Rohde, Manfred, Pukall, Ruediger, Goeker, Markus, Detter, John C., Woyke, Tanja, Bristow, James, Eisen, Jonathan A. ... Mavromatis, Konstantinos (2012). Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). Standards in Genomic Sciences, 6 (3), 293-303. doi: 10.4056/sigs.2736042